How can I fill up my toilet model with water?
In Edit Mode select an Edge Loop at a location where you want the top of the water to be.



Duplicate it SHFT+D Then separate it by pressing P > Selection.

TAB into Object Mode and select the object you just created (I hid the other objects).

TAB  into Edit Mode and Extrude these vertices inward as in the imageE  SSHFTZ



Select all of the vertices except the outer edge and move them down a bit G Z This creates the "meniscus".



You will want a Subsurf Modifier and Smooth Shading.

Here is my Node Setup for the material.